Dependency issues after adding new sources.

[Dave Steenburgh]

Please excuse my ignorance, but my search fu is weak, and I think the
authors of tfm are conspiring to bewilder me.  I have read several tutorials
and discussions on how to use the autotools, but to be honest my
understanding of them is extremely limited at best.
I have this problem with several of my programs, but it's most frustrating
with my current program, which at the moment has a flat directory structure.
 The program in question is developed little by little, so from time to time
I need to add new source files to the program's _SOURCES in Makefile.am.  I
was under the impression that after doing so, running make from the build
directory would magically figure everything out and build the program
correctly.  What happens instead is the Makefile appears to be regenerated,
but my new sources are not included in it.  I have tried multiple methods to
fix this, most of them to no avail.  Currently, the new sources are built
and are linked into the executable, but most of the old sources aren't being
rebuilt when a common header is changed.  The only thing that fixes all the
issues is to start with an empty build directory and re-run the configure
script.  I doubt that it's really necessary to create a new build directory
every time I add a new class.  So what could I be doing wrong?  I will
gladly share any information about my build environment that may help a
diagnosis, but I'd prefer to keep the code private.